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Yorodumi- EMDB-14391: Endonuclease state of the E. coli Mre11-Rad50 (SbcCD) head comple... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14391 | |||||||||
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Title | Endonuclease state of the E. coli Mre11-Rad50 (SbcCD) head complex bound to ADP and dsDNA | |||||||||
Map data | ||||||||||
Sample |
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Keywords | ABC-type ATPase / Nuclease / DNA repair / DNA BINDING PROTEIN | |||||||||
Function / homology | Function and homology information double-stranded DNA endonuclease activity / DNA exonuclease activity / single-stranded DNA endodeoxyribonuclease activity / 3'-5'-DNA exonuclease activity / DNA repair complex / 3'-5' exonuclease activity / double-strand break repair / DNA recombination / DNA replication / DNA repair ...double-stranded DNA endonuclease activity / DNA exonuclease activity / single-stranded DNA endodeoxyribonuclease activity / 3'-5'-DNA exonuclease activity / DNA repair complex / 3'-5' exonuclease activity / double-strand break repair / DNA recombination / DNA replication / DNA repair / ATP hydrolysis activity / DNA binding / ATP binding Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Gut F / Kaeshammer L | |||||||||
Funding support | European Union, Germany, 2 items
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Citation | Journal: Mol Cell / Year: 2022 Title: Structural mechanism of endonucleolytic processing of blocked DNA ends and hairpins by Mre11-Rad50. Authors: Fabian Gut / Lisa Käshammer / Katja Lammens / Joseph D Bartho / Anna-Maria Boggusch / Erik van de Logt / Brigitte Kessler / Karl-Peter Hopfner / Abstract: DNA double-strand breaks (DSBs) threaten genome stability and are linked to tumorigenesis in humans. Repair of DSBs requires the removal of attached proteins and hairpins through a poorly understood ...DNA double-strand breaks (DSBs) threaten genome stability and are linked to tumorigenesis in humans. Repair of DSBs requires the removal of attached proteins and hairpins through a poorly understood but physiologically critical endonuclease activity by the Mre11-Rad50 complex. Here, we report cryoelectron microscopy (cryo-EM) structures of the bacterial Mre11-Rad50 homolog SbcCD bound to a protein-blocked DNA end and a DNA hairpin. The structures reveal that Mre11-Rad50 bends internal DNA for endonucleolytic cleavage and show how internal DNA, DNA ends, and hairpins are processed through a similar ATP-regulated conformational state. Furthermore, Mre11-Rad50 is loaded onto blocked DNA ends with Mre11 pointing away from the block, explaining the distinct biochemistries of 3' → 5' exonucleolytic and endonucleolytic incision through the way Mre11-Rad50 interacts with diverse DNA ends. In summary, our results unify Mre11-Rad50's enigmatic nuclease diversity within a single structural framework and reveal how blocked DNA ends and hairpins are processed. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_14391.map.gz | 7.5 MB | EMDB map data format | |
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Header (meta data) | emd-14391-v30.xml emd-14391.xml | 21.9 KB 21.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_14391_fsc.xml | 11.4 KB | Display | FSC data file |
Images | emd_14391.png | 123.8 KB | ||
Masks | emd_14391_msk_1.map | 125 MB | Mask map | |
Filedesc metadata | emd-14391.cif.gz | 6.9 KB | ||
Others | emd_14391_additional_1.map.gz emd_14391_half_map_1.map.gz emd_14391_half_map_2.map.gz | 951.6 MB 98.4 MB 98.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14391 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14391 | HTTPS FTP |
-Validation report
Summary document | emd_14391_validation.pdf.gz | 726.8 KB | Display | EMDB validaton report |
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Full document | emd_14391_full_validation.pdf.gz | 726.4 KB | Display | |
Data in XML | emd_14391_validation.xml.gz | 18.5 KB | Display | |
Data in CIF | emd_14391_validation.cif.gz | 24.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14391 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14391 | HTTPS FTP |
-Related structure data
Related structure data | 7yzoMC 7yzpC 7z03C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_14391.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.059 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_14391_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: LAFTER-filtered cryo-EM map
File | emd_14391_additional_1.map | ||||||||||||
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Annotation | LAFTER-filtered cryo-EM map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_14391_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_14391_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Complex of Mre11 dimer, Rad50 dimer and double-stranded DNA
Entire | Name: Complex of Mre11 dimer, Rad50 dimer and double-stranded DNA |
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Components |
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-Supramolecule #1: Complex of Mre11 dimer, Rad50 dimer and double-stranded DNA
Supramolecule | Name: Complex of Mre11 dimer, Rad50 dimer and double-stranded DNA type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: Escherichia coli (E. coli) |
-Macromolecule #1: Nuclease SbcCD subunit C
Macromolecule | Name: Nuclease SbcCD subunit C / type: protein_or_peptide / ID: 1 Details: A large part of the structure in the middle of the sequence is missing. Therefore the alignment is not correct. The C-terminal part misaligns to the middle domain of the sequence. Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 118.851508 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MKILSLRLKN LNSLKGEWKI DFTREPFASN GLFAITGPTG AGKTTLLDAI CLALYHETPR LSNVSQSQND LMTRDTAECL AEVEFEVKG EAYRAFWSQN RARNQPDGNL QVPRVELARC ADGKILADKV KDKLELTATL TGLDYGRFTR SMLLSQGQFA A FLNAKPKE ...String: MKILSLRLKN LNSLKGEWKI DFTREPFASN GLFAITGPTG AGKTTLLDAI CLALYHETPR LSNVSQSQND LMTRDTAECL AEVEFEVKG EAYRAFWSQN RARNQPDGNL QVPRVELARC ADGKILADKV KDKLELTATL TGLDYGRFTR SMLLSQGQFA A FLNAKPKE RAELLEELTG TEIYGQISAM VFEQHKSART ELEKLQAQAS GVTLLTPEQV QSLTASLQVL TDEEKQLITA QQ QEQQSLN WLTRQDELQQ EASRRQQALQ QALAEEEKAQ PQLAALSLAQ PARNLRPHWE RIAEHSAALA HIRQQIEEVN TRL QSTMAL RASIRHHAAK QSAELQQQQQ SLNTWLQEHD RFRQWNNEPA GWRAQFSQQT SDREHLRQWQ QQLTHAEQKL NALA AITLT LTADEVATAL AQHAEQRPLR QHLVALHGQI VPQQKRLAQL QVAIQNVTQE QTQRNAALNE MRQRYKEKTQ QLADV KTIC EQEARIKTLE AQRAQLQAGQ PCPLCGSTSH PAVEAYQALE PGVNQSRLLA LENEVKKLGE EGATLRGQLD AITKQL QRD ENEAQSLRQD EQALTQQWQA VTASLNITLQ PLDDIQPWLD AQDEHERQLR LLSQRHELQG QIAAHNQQII QYQQQIE QR QQLLLTTLTG YALTLPQEDE EESWLATRQQ EAQSWQQRQN ELTALQNRIQ QLTPILETLP QSDELPHCEE TVVLENWR Q VHEQCLALHS QQQTLQQQDV LAAQSLQKAQ AQFDTALQAS VFDDQQAFLA ALMDEQTLTQ LEQLKQNLEN QRRQAQTLV TQTAETLAQH QQHRPDDGLA LTVTVEQIQQ ELAQTHQKLR ENTTSQGEIR QQLKQDADNR QQQQTLMQQI AQMTQQVEDW GYLNSLIGS KEGDKFRKFA QGLTLDNLVH LANQQLTRLH GRYLLQRKAS EALEVEVVDT WQADAVRDTR TLSGGESFLV S LALALALS DLVSHKTRID SLFLDEGFGT LDSETLDTAL DALDALNASG KTIGVISHVE AMKERIPVQI KVKKINGLGY SK LESTFAV K UniProtKB: Nuclease SbcCD subunit C |
-Macromolecule #2: Nuclease SbcCD subunit D
Macromolecule | Name: Nuclease SbcCD subunit D / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 45.640277 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MRILHTSDWH LGQNFYSKSR EAEHQAFLDW LLETAQTHQV DAIIVAGDVF DTGSPPSYAR TLYNRFVVNL QQTGCHLVVL AGNQDSVAT LNESRDIMAF LNTTVVASAG HAPQILPRRD GTPGAVLCPI PFLRPRDIIT SQAGLNGIEK QQHLLAAITD Y YQQHYADA ...String: MRILHTSDWH LGQNFYSKSR EAEHQAFLDW LLETAQTHQV DAIIVAGDVF DTGSPPSYAR TLYNRFVVNL QQTGCHLVVL AGNQDSVAT LNESRDIMAF LNTTVVASAG HAPQILPRRD GTPGAVLCPI PFLRPRDIIT SQAGLNGIEK QQHLLAAITD Y YQQHYADA CKLRGDQPLP IIATGHLTTV GASKSDAVRD IYIGTLDAFP AQNFPPADYI ALGHIHRAQI IGGMEHVRYC GS PIPLSFD ECGKSKYVHL VTFSNGKLES VENLNVPVTQ PMAVLKGDLA SITAQLEQWR DVSQEPPVWL DIEITTDEYL HDI QRKIQA LTESLPVEVL LVRRSREQRE RVLASQQRET LSELSVEEVF NRRLALEELD ESQQQRLQHL FTTTLHTLAG EHEA GHHHH HH UniProtKB: Nuclease SbcCD subunit D |
-Macromolecule #3: DNA (31-MER)
Macromolecule | Name: DNA (31-MER) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 37.099617 KDa |
Sequence | String: (DC)(DC)(DA)(DG)(DT)(DT)(DG)(DA)(DT)(DC) (DG)(DG)(DC)(DG)(DC)(DG)(DA)(DG)(DA)(DT) (DT)(DT)(DA)(DA)(DT)(DC)(DG)(DC)(DC) (DG)(DC)(DG)(DA)(DC)(DA)(DA)(DT)(DT)(DT) (DG) (DC)(DG)(DA)(DC)(DG)(DG) ...String: (DC)(DC)(DA)(DG)(DT)(DT)(DG)(DA)(DT)(DC) (DG)(DG)(DC)(DG)(DC)(DG)(DA)(DG)(DA)(DT) (DT)(DT)(DA)(DA)(DT)(DC)(DG)(DC)(DC) (DG)(DC)(DG)(DA)(DC)(DA)(DA)(DT)(DT)(DT) (DG) (DC)(DG)(DA)(DC)(DG)(DG)(DC)(DG) (DC)(DG)(DT)(DG)(DC)(DA)(DG)(DG)(DG)(DC) (DC)(DA) (DG)(DA)(DC)(DT)(DG)(DG)(DA) (DG)(DG)(DT)(DG)(DG)(DC)(DA)(DA)(DC)(DG) (DC)(DC)(DA) (DA)(DT)(DC)(DA)(DG)(DC) (DA)(DA)(DC)(DG)(DA)(DC)(DT)(DG)(DT)(DT) (DT)(DG)(DC)(DC) (DC)(DG)(DC)(DC)(DA) (DG)(DT)(DT)(DG)(DT)(DT)(DG)(DT)(DG)(DC) (DC)(DA)(DC)(DG)(DC) GENBANK: GENBANK: MN982376.1 |
-Macromolecule #4: DNA (31-MER)
Macromolecule | Name: DNA (31-MER) / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 36.970527 KDa |
Sequence | String: (DG)(DC)(DG)(DT)(DG)(DG)(DC)(DA)(DC)(DA) (DA)(DC)(DA)(DA)(DC)(DT)(DG)(DG)(DC)(DG) (DG)(DG)(DC)(DA)(DA)(DA)(DC)(DA)(DG) (DT)(DC)(DG)(DT)(DT)(DG)(DC)(DT)(DG)(DA) (DT) (DT)(DG)(DG)(DC)(DG)(DT) ...String: (DG)(DC)(DG)(DT)(DG)(DG)(DC)(DA)(DC)(DA) (DA)(DC)(DA)(DA)(DC)(DT)(DG)(DG)(DC)(DG) (DG)(DG)(DC)(DA)(DA)(DA)(DC)(DA)(DG) (DT)(DC)(DG)(DT)(DT)(DG)(DC)(DT)(DG)(DA) (DT) (DT)(DG)(DG)(DC)(DG)(DT)(DT)(DG) (DC)(DC)(DA)(DC)(DC)(DT)(DC)(DC)(DA)(DG) (DT)(DC) (DT)(DG)(DG)(DC)(DC)(DC)(DT) (DG)(DC)(DA)(DC)(DG)(DC)(DG)(DC)(DC)(DG) (DT)(DC)(DG) (DC)(DA)(DA)(DA)(DT)(DT) (DG)(DT)(DC)(DG)(DC)(DG)(DG)(DC)(DG)(DA) (DT)(DT)(DA)(DA) (DA)(DT)(DC)(DT)(DC) (DG)(DC)(DG)(DC)(DC)(DG)(DA)(DT)(DC)(DA) (DA)(DC)(DT)(DG)(DG) GENBANK: GENBANK: MN982376.1 |
-Macromolecule #5: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 2 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ChemComp-ADP: |
-Macromolecule #6: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 2 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #7: MANGANESE (II) ION
Macromolecule | Name: MANGANESE (II) ION / type: ligand / ID: 7 / Number of copies: 4 / Formula: MN |
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Molecular weight | Theoretical: 54.938 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 43.19 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 1.2 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |